Once you mentioned the directories I went and looked and apparently there was a calibre directory on my duopro card so basically I deleted everything and started over and so far it seems to be working. Not sure how that happened...but I've been having some weirdness since I updated the Sony Reader software.

Okay it seems that around 348 files added to the memory card Calibre gives me the error message and won't let me add any more stories, which is weird because I used to have over 1000 files on the memory card.

No - it is not normally possible to re-format the cards to another format.

Have you actually tried re-formatting the card rather than simply deleting the files? That might reclaim some lost space.

I hadn't reformatted because it still shows i have 1.6 gigs of free space left on the drive. So it just seems weird that it would have run out of space. But I'm desperate and at this point will try anything.